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Complex of escherichia COLI DNA adenine methyltransferase (dam) with sah and with DNA containing distal pap regulon sequence

Analyse Complex of escherichia COLI DNA adenine methyltransferase (dam) with sah and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4RTK
Type
protein + DNA
Length
267 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA adenine methylase; DNA (5'-D(*TP*CP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3'); DNA…
UniProt
H0Q7C9
Ligands
SAH
Pockets
1 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA adenine methylaseprotein24543% helix, 17% strandH0Q7C9
FDNA (5'-D(*TP*CP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3')dna11——
GDNA (5'-D(*AP*CP*GP*AP*TP*CP*TP*TP*TP*AP*G)-3')dna11——

Ligands and binding sites

  • SAH · S-adenosyl-L-homocysteine · ligand · chains A
  • GOL · Glycerol · additive · chains A, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13210.600.7844SAH

Interfaces

3 interfaces between chains.

  • F–G · 449 Ų buried · 38 hydrogen bonds · nucleic-nucleic
  • A–G · 309 Ų buried · 9 hydrogen bonds · protein-nucleic
  • A–F · 34 Ų buried · 0 hydrogen bonds · protein-nucleic

Compared structures

  • 4RTK · Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) with SAH and with DNA… · the same entry in another collection · chain A against A, TM-score 1.00

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